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<p>Dear Matt<br>
</p>
<div class="moz-cite-prefix">Il 25/10/24 01:02, Matthew Knepley ha
scritto:<br>
</div>
<blockquote type="cite" cite="mid:CAMYG4Gnzta4wzkL4CBGG7WO4bi0mi=zyQ0myxU_xG5ZaJhmx5Q@mail.gmail.com">
<div dir="ltr">
<div dir="ltr">On Thu, Oct 24, 2024 at 6:04 PM Matteo Semplice
<<a href="mailto:matteo.semplice@uninsubria.it" moz-do-not-send="true" class="moz-txt-link-freetext">matteo.semplice@uninsubria.it</a>>
wrote:</div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi. The HDF5 solution looks good to me, but I now get
this error<br>
</p>
<p><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"></span></span></p>
</div>
</blockquote>
<div>Okay, I can make a workaround for this. Here is what is
happening.</div>
<div><br>
</div>
<div>When you output solutions, you really want the essential
boundary conditions included in the</div>
<div>output, and the only way I have to do that is for you to
tell me about the discretization, so I</div>
<div>require the DS.</div>
<div><br>
</div>
<div>What I can do is ignore this step if there is no DS. Let
me do that and mail you with the branch.</div>
</div>
</div>
</blockquote>
<p>Sorry for the long delay, but now I am taking this up again.<br>
</p>
<p>In my code I compute all fields in all cells and I have no
boundary conditions. I tried to just call DMCreateDS on the mesh,
but the error does not change. I guess that I need to do a minimal
setup on the DS to have it working.<br>
</p>
<p>If you have some time, could you create the branch you mentioned
in your message or tell me what is the minimal action I have to do
to setup a "fake" ds? Whichever is the best for you is fine with
me.<br>
</p>
<p>If you need more info, in my Section I have 3 fields attached to
cells. I have also another dm with a field attached to vertices,
but this latter is less important and I don't really need it in
output for production runs.<br>
</p>
<p>Thanks</p>
<p> Matteo<br>
</p>
<blockquote type="cite" cite="mid:CAMYG4Gnzta4wzkL4CBGG7WO4bi0mi=zyQ0myxU_xG5ZaJhmx5Q@mail.gmail.com">
<div dir="ltr">
<div class="gmail_quote">
<div><br>
</div>
<div> Thanks!</div>
<div><br>
</div>
<div> Matt </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">$
../src/saveDemo </span><br>
Creating mesh with (10,10) faces <br>
<span style="font-weight:bold;color:rgb(255,84,84);background-color:rgb(255,255,255)">[0]PETSC
ERROR: --------------------- Error Message
--------------------------------------------------------------</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> </span><br>
[0]PETSC ERROR: Object is in wrong state <br>
[0]PETSC ERROR: Need to call DMCreateDS() before
calling DMGetDS() <br>
[0]PETSC ERROR: See <a href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!f3xcC-P6ZKjh4GKu4oz9-xo0-soAZzH97UszdXrhFrCLfp14uEixVvm8ME-t8J1qTOJY50bopUUkRuerZImYSYMcYOyMJjVPxoR1-Q$" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://petsc.org/release/faq/</a>
for trouble shooting. <br>
[0]PETSC ERROR: Petsc Release Version 3.21.5, unknown
<br>
[0]PETSC ERROR: ../src/saveDemo on a named
dentdherens by matteo Fri Oct 25 00:00:44 2024 <br>
[0]PETSC ERROR: Configure options --COPTFLAGS="-O3
-march=native -mtune=native -mavx2" --CXXOPTFLAGS="-O3
-march=native -mtune=native -mavx2" --FOPTFLAGS="-O3
-march=native -mtune=native -mavx2" --PETSC_ARCH=op<br>
t --with-strict-petscerrorcode --download-hdf5
--prefix=/home/matteo/software/petsc/3.21-opt/
--with-debugging=0 --with-gmsh --with-metis
--with-parmetis --with-triangle
PETSC_DIR=/home/matteo/software/petsc --<br>
force <br>
[0]PETSC ERROR: #1 DMGetDS() at
/home/matteo/software/petsc/src/dm/interface/dm.c:5525
<br>
[0]PETSC ERROR: #2 DMPlexInsertBoundaryValues_Plex()
at
/home/matteo/software/petsc/src/dm/impls/plex/plexfem.c:1136
<br>
[0]PETSC ERROR: #3 DMPlexInsertBoundaryValues() at
/home/matteo/software/petsc/src/dm/impls/plex/plexfem.c:1274
<br>
[0]PETSC ERROR: #4 VecView_Plex_HDF5_Internal() at
/home/matteo/software/petsc/src/dm/impls/plex/plexhdf5.c:477
<br>
[0]PETSC ERROR: #5 VecView_Plex() at
/home/matteo/software/petsc/src/dm/impls/plex/plex.c:656
<br>
[0]PETSC ERROR: #6 VecView() at
/home/matteo/software/petsc/src/vec/vec/interface/vector.c:806
<br>
[0]PETSC ERROR: #7 main() at saveDemo.cpp:123 <br>
[0]PETSC ERROR: No PETSc Option Table entries <br>
<span style="font-weight:bold;color:rgb(255,84,84);background-color:rgb(255,255,255)">[0]PETSC
ERROR: ----------------End of Error Message
-------send entire error message to <a href="mailto:petsc-maint@mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">petsc-maint@mcs.anl.gov</a>----------</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> </span><br>
--------------------------------------------------------------------------
<br>
MPI_ABORT was invoked on rank 0 in communicator
MPI_COMM_SELF <br>
with errorcode 73. <br>
<br>
NOTE: invoking MPI_ABORT causes Open MPI to kill all
MPI processes. <br>
You may or may not see output from other processes,
depending on <br>
exactly when Open MPI kills them. <br>
--------------------------------------------------------------------------<br>
</span></p>
<p>I attach the modified sample code that produced the
above error.<br>
</p>
<p>Thanks</p>
<p> Matteo<br>
</p>
<div>Il 24/10/24 22:20, Matthew Knepley ha scritto:<br>
</div>
<blockquote type="cite">
<div dir="ltr">I just looked at the code. The VTK code
is very old, and does not check for cell overlap.
<div><br>
</div>
<div>We have been recommending that people use either
HDF5 or CGNS, both of which work in this case</div>
<div>I believe. I can fix VTK if that is what you
want, but it might take me a little while as it is
very busy at</div>
<div>work right now. However, if you output HDF5, then
you can run</div>
<div><br>
</div>
<div> ./lib/petsc/bin/petsc_gen_xdmf.py mesh.h5</div>
<div><br>
</div>
<div>and it will generate an XDMF file so you can load
it into ParaView. Or you can output CGNS which I
think</div>
<div>ParaView understands.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Oct 24, 2024
at 4:02 PM Semplice Matteo <<a href="mailto:matteo.semplice@uninsubria.it" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">matteo.semplice@uninsubria.it</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Hi,</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
I tried again today and have
(re?)discovered this example <a href="https://urldefense.us/v3/__https://petsc.org/release/src/dm/impls/plex/tutorials/ex14.c.html__;!!G_uCfscf7eWS!f3xcC-P6ZKjh4GKu4oz9-xo0-soAZzH97UszdXrhFrCLfp14uEixVvm8ME-t8J1qTOJY50bopUUkRuerZImYSYMcYOyMJjVM1k_vVQ$" id="m_2093919128985184015m_5982902773776001898LPlnk382398" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">
https://petsc.org/release/src/dm/impls/plex/tutorials/ex14.c.html</a>,
but I cannot understand if in my case I should
call <a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/PetscSF/PetscSFCreateSectionSF/__;!!G_uCfscf7eWS!f3xcC-P6ZKjh4GKu4oz9-xo0-soAZzH97UszdXrhFrCLfp14uEixVvm8ME-t8J1qTOJY50bopUUkRuerZImYSYMcYOyMJjXAq_GDrQ$" id="m_2093919128985184015m_5982902773776001898OWA7823b4db-9caf-edfa-8c7d-7a06e4a231c3" target="_blank" moz-do-not-send="true">
PetscSFCreateSectionSF</a> and, if so, how
should I then activate the returned SF.</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Matteo</div>
<hr style="display:inline-block;width:98%">
<div id="m_2093919128985184015m_5982902773776001898divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>Da:</b>
Semplice Matteo<br>
<b>Inviato:</b> martedì 22 ottobre 2024
00:24<br>
<b>A:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">knepley@gmail.com</a>><br>
<b>Cc:</b> PETSc <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">petsc-users@mcs.anl.gov</a>><br>
<b>Oggetto:</b> Re: [petsc-users]
local/global DMPlex Vec output</font>
<div> </div>
</div>
<div>
<p>Dear Matt,</p>
<p> I guess you're right: thresholding by
rank==0 and rank==1 in paraview reveals that
it is indeed the overlap cells that are
appear twice in the output.<br>
</p>
<p>The attached file is not exactly minimal
but hopefully short enough. If I run it in
serial, all is ok, but with</p>
<p> mpirun -np 2 ./saveDemo</p>
<p>it creates a 10x10 grid, but I get
"output.vtu" with a total of 120 cells.
However the pointSF of the DMPlex seems
correct.</p>
<p>Thanks</p>
<p> Matteo<br>
</p>
<div>Il 21/10/24 19:15, Matthew Knepley ha
scritto:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Mon, Oct 21, 2024 at
12:22 PM Matteo Semplice via petsc-users
<<a href="mailto:petsc-users@mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">petsc-users@mcs.anl.gov</a>>
wrote:<br>
</div>
<div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Dear petsc-users,<br>
</p>
<p> I am having issues with
output of parallel data attached
to a DMPlex (or maybe more
fundamental ones about DMPlex...).</p>
<p>So I currently</p>
<ol>
<li>create a DMPlex
(DMPlexCreateGmshFromFile or
DMPlexCreateBoxMesh)</li>
<li>partition it</li>
<li>and create a section for my
data layout with
DMPlexCreateSection(ctx.dmMesh,
NULL, numComp, numDof, numBC,
NULL, NULL, NULL, NULL,
&sUavg)</li>
<li>DMSetLocalSection(ctx.dmMesh,
sUavg)</li>
<li>create solLoc and solGlob
vectors with
DMCreateGlobalVector and
DMCreateLocalVector</li>
<li>solve ....</li>
<li>VecView(ctx.solGlob,
vtkViewer) on a .vtu file<br>
</li>
</ol>
<p>but when I load data in ParaView
I get more cells than expected and
it is as if the cells in the halo
are put twice in output. (I could
create a MWE if the above is not
clear)<br>
</p>
</div>
</blockquote>
<div>I think we need an MWE here,
because from the explanation above, it
should work.</div>
<div><br>
</div>
<div>However, I can try to guess the
problem. When you partition the mesh,
I am guessing that you have cells in
the overlap. These cells</div>
<div>must be in the point SF in order
for the global section to give them a
unique owner. Perhaps something has
gone wrong here.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt </div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>I guess that the culprit is point
(4), but if I replace it with
DMSetGlobalSection then I cannot
create the local vector at point
(5).<br>
</p>
<p>How should I handle this
properly? In my code I need to
create both local and global
vectors, to perform at least
GlobalToLocal and to save the
global data.<br>
</p>
<p>(On a side note, I tried also
HDF5 but then it complains about
the DM not having a DS...; really,
any working solution that allows
data to be explored with Paraview
is fine)<br>
</p>
<p>Thanks for any advice!<br>
</p>
<p>Matteo Semplice</p>
</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
<span>-- </span><br>
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<div dir="ltr">
<div>
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<div>
<div dir="ltr">
<div>What most experimenters
take for granted before they
begin their experiments is
infinitely more interesting
than any results to which
their experiments lead.<br>
-- Norbert Wiener</div>
<div><br>
</div>
<div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!f3xcC-P6ZKjh4GKu4oz9-xo0-soAZzH97UszdXrhFrCLfp14uEixVvm8ME-t8J1qTOJY50bopUUkRuerZImYSYMcYOyMJjUhSnQjTQ$" target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
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</div>
</blockquote>
<pre cols="72">--
---
Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como</pre>
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<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>What most experimenters take for
granted before they begin their
experiments is infinitely more interesting
than any results to which their
experiments lead.<br>
-- Norbert Wiener</div>
<div><br>
</div>
<div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!f3xcC-P6ZKjh4GKu4oz9-xo0-soAZzH97UszdXrhFrCLfp14uEixVvm8ME-t8J1qTOJY50bopUUkRuerZImYSYMcYOyMJjUhSnQjTQ$" target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
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</blockquote>
<pre cols="72">--
---
Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como</pre>
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<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>What most experimenters take for granted before
they begin their experiments is infinitely more
interesting than any results to which their
experiments lead.<br>
-- Norbert Wiener</div>
<div><br>
</div>
<div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!f3xcC-P6ZKjh4GKu4oz9-xo0-soAZzH97UszdXrhFrCLfp14uEixVvm8ME-t8J1qTOJY50bopUUkRuerZImYSYMcYOyMJjUhSnQjTQ$" target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
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<pre class="moz-signature" cols="72">--
---
Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como</pre>
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